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Tolbatov I, Umari P, Marrone A. Diruthenium Paddlewheel Complexes Attacking Proteins: Axial versus Equatorial Coordination. Biomolecules 2024; 14:530. [PMID: 38785937 PMCID: PMC11117738 DOI: 10.3390/biom14050530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Metallodrugs are an important group of medicinal agents used for the treatment of various diseases ranging from cancers to viral, bacterial, and parasitic diseases. Their distinctive features include the availability of a metal centre, redox activity, as well as the ability to multitarget. Diruthenium paddlewheel complexes are an intensely developing group of metal scaffolds, which can securely coordinate bidentate xenobiotics and transport them to target tissues, releasing them by means of substitution reactions with biomolecular nucleophiles. It is of the utmost importance to gain a complete comprehension of which chemical reactions happen with them in physiological milieu to design novel drugs based on these bimetallic scaffolds. This review presents the data obtained in experiments and calculations, which clarify the chemistry these complexes undergo once administered in the proteic environment. This study demonstrates how diruthenium paddlewheel complexes may indeed embody a new paradigm in the design of metal-based drugs of dual-action by presenting and discussing the protein metalation by these complexes.
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Affiliation(s)
- Iogann Tolbatov
- Department of Physics and Astronomy, University of Padova, Via F. Marzolo 8, 35131 Padova, Italy;
| | - Paolo Umari
- Department of Physics and Astronomy, University of Padova, Via F. Marzolo 8, 35131 Padova, Italy;
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università “G d’Annunzio” di Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
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Sun X, Huang X, Park KS, Zhou X, Kennedy AA, Pretto CD, Wu Q, Wan Z, Xu Y, Gong W, Sexton JZ, Tai AW, Lei YL, Moon JJ. Self-Assembled STING-Activating Coordination Nanoparticles for Cancer Immunotherapy and Vaccine Applications. ACS NANO 2024; 18:10439-10453. [PMID: 38567994 PMCID: PMC11031738 DOI: 10.1021/acsnano.3c11374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The cGAS-STING pathway plays a crucial role in innate immune activation against cancer and infections, and STING agonists based on cyclic dinucleotides (CDN) have garnered attention for their potential use in cancer immunotherapy and vaccines. However, the limited drug-like properties of CDN necessitate an efficient delivery system to the immune system. To address these challenges, we developed an immunostimulatory delivery system for STING agonists. Here, we have examined aqueous coordination interactions between CDN and metal ions and report that CDN mixed with Zn2+ and Mn2+ formed distinctive crystal structures. Further pharmaceutical engineering led to the development of a functional coordination nanoparticle, termed the Zinc-Mn-CDN Particle (ZMCP), produced by a simple aqueous one-pot synthesis. Local or systemic administration of ZMCP exerted robust antitumor efficacy in mice. Importantly, recombinant protein antigens from SARS-CoV-2 can be simply loaded during the aqueous one-pot synthesis. The resulting ZMCP antigens elicited strong cellular and humoral immune responses that neutralized SARS-CoV-2, highlighting ZMCP as a self-adjuvant vaccine platform against COVID-19 and other infectious pathogens. Overall, this work establishes a paradigm for developing translational coordination nanomedicine based on drug-metal ion coordination and broadens the applicability of coordination medicine for the delivery of proteins and other biologics.
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Affiliation(s)
- Xiaoqi Sun
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xuehui Huang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyung Soo Park
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xingwu Zhou
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew A Kennedy
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Carla D Pretto
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Qi Wu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ziye Wan
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yao Xu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wang Gong
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Cancer Biology at the University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, United States
| | - Jonathan Z Sexton
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew W Tai
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Otolaryngology─Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Head and Neck Surgery, Department of Cancer Biology, Department of Translational Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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Wong KY, Nie Z, Wong MS, Wang Y, Liu J. Metal-Drug Coordination Nanoparticles and Hydrogels for Enhanced Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2404053. [PMID: 38602715 DOI: 10.1002/adma.202404053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/08/2024] [Indexed: 04/12/2024]
Abstract
Drug delivery is a key component of nanomedicine, and conventional delivery relies on the adsorption or encapsulation of drug molecules to a nanomaterial. Many delivery vehicles contain metal ions, such as metal-organic frameworks, metal oxides, transition metal dichalcogenides, MXene, and noble metal nanoparticles. These materials have a high metal content and pose potential long-term toxicity concerns leading to difficulties for clinical approval. In this review, recent developments are summarized in the use of drug molecules as ligands for metal coordination forming various nanomaterials and soft materials. In these cases, the drug-to-metal ratio is much higher than conventional adsorption-based strategies. The drug molecules are divided into small-molecule drugs, nucleic acids, and proteins. The formed hybrid materials mainly include nanoparticles and hydrogels, upon which targeting ligands can be grafted to improve efficacy and further decrease toxicity. The application of these materials for addressing cancer, viral infection, bacterial infection inflammatory bowel disease, and bone diseases is reviewed. In the end, some future directions are discussed from fundamental research, materials science, and medicine.
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Affiliation(s)
- Ka-Ying Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Centre for Eye and Vision Research (CEVR), 17W, Hong Kong Science Park, Pak Shek Kok, 999077, Hong Kong
| | - Zhenyu Nie
- Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha , 410008, P. R. China
| | - Man-Sau Wong
- Centre for Eye and Vision Research (CEVR), 17W, Hong Kong Science Park, Pak Shek Kok, 999077, Hong Kong
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, 999077, Hong Kong
- Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, 999077, Hong Kong
| | - Yang Wang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha , 410008, P. R. China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Centre for Eye and Vision Research (CEVR), 17W, Hong Kong Science Park, Pak Shek Kok, 999077, Hong Kong
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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5
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York DM. Modern Alchemical Free Energy Methods for Drug Discovery Explained. ACS PHYSICAL CHEMISTRY AU 2023; 3:478-491. [PMID: 38034038 PMCID: PMC10683484 DOI: 10.1021/acsphyschemau.3c00033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 12/02/2023]
Abstract
This Perspective provides a contextual explanation of the current state-of-the-art alchemical free energy methods and their role in drug discovery as well as highlights select emerging technologies. The narrative attempts to answer basic questions about what goes on "under the hood" in free energy simulations and provide general guidelines for how to run simulations and analyze the results. It is the hope that this work will provide a valuable introduction to students and scientists in the field.
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Affiliation(s)
- Darrin M. York
- Laboratory for Biomolecular
Simulation Research, Institute for Quantitative Biomedicine, and Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
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Yang D, Zhang Y, Sow IS, Liang H, El Manssouri N, Gelbcke M, Dong L, Chen G, Dufrasne F, Fontaine V, Li R. Antimycobacterial Activities of Hydroxamic Acids and Their Iron(II/III), Nickel(II), Copper(II) and Zinc(II) Complexes. Microorganisms 2023; 11:2611. [PMID: 37894269 PMCID: PMC10609363 DOI: 10.3390/microorganisms11102611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Hydroxamic acid (HA) derivatives display antibacterial and antifungal activities. HA with various numbers of carbon atoms (C2, C6, C8, C10, C12 and C17), complexed with different metal ions, including Fe(II/III), Ni(II), Cu(II) and Zn(II), were evaluated for their antimycobacterial activities and their anti-biofilm activities. Some derivatives showed antimycobacterial activities, especially in biofilm growth conditions. For example, 20-100 µM of HA10Fe2, HA10FeCl, HA10Fe3, HA10Ni2 or HA10Cu2 inhibited Mycobacterium tuberculosis, Mycobacterium bovis BCG and Mycobacterium marinum biofilm development. HA10Fe2, HA12Fe2 and HA12FeCl could even attack pre-formed Pseudomonas aeruginosa biofilms at higher concentrations (around 300 µM). The phthiocerol dimycocerosate (PDIM)-deficient Mycobacterium tuberculosis H37Ra was more sensitive to the ion complexes of HA compared to other mycobacterial strains. Furthermore, HA10FeCl could increase the susceptibility of Mycobacterium bovis BCG to vancomycin. Proteomic profiles showed that the potential targets of HA10FeCl were mainly related to mycobacterial stress adaptation, involving cell wall lipid biosynthesis, drug resistance and tolerance and siderophore metabolism. This study provides new insights regarding the antimycobacterial activities of HA and their complexes, especially about their potential anti-biofilm activities.
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Affiliation(s)
- Dong Yang
- Clinical Laboratory, Shanxi Provincial People’s Hospital, Affiliated of Shanxi Medical University, Taiyuan 030001, China; (D.Y.)
| | - Yanfang Zhang
- Clinical Laboratory, Shanxi Provincial People’s Hospital, Affiliated of Shanxi Medical University, Taiyuan 030001, China; (D.Y.)
| | - Ibrahima Sory Sow
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium; (I.S.S.); (V.F.)
| | - Hongping Liang
- Clinical Laboratory, Shanxi Provincial People’s Hospital, Affiliated of Shanxi Medical University, Taiyuan 030001, China; (D.Y.)
| | - Naïma El Manssouri
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium; (I.S.S.); (V.F.)
| | - Michel Gelbcke
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium; (I.S.S.); (V.F.)
| | - Lina Dong
- Core Laboratory, Shanxi Provincial People’s Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan 030012, China
| | - Guangxin Chen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - François Dufrasne
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium; (I.S.S.); (V.F.)
| | - Véronique Fontaine
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium; (I.S.S.); (V.F.)
| | - Rongshan Li
- Department of Nephrology, Shanxi Kidney Disease Institute, The Affiliated People’s Hospital of Shanxi Medical University, Shanxi Provincial People’s Hospital, Taiyuan 030001, China
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Buikin P, Vologzhanina A, Novikov R, Dorovatovskii P, Korlyukov A. Abiraterone Acetate Complexes with Biometals: Synthesis, Characterization in Solid and Solution, and the Nature of Chemical Bonding. Pharmaceutics 2023; 15:2180. [PMID: 37765151 PMCID: PMC10535913 DOI: 10.3390/pharmaceutics15092180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Abiraterone acetate (AbirAc) is the most used steroidal therapeutic agent for treatment of prostate cancer. The mainly hydrophobic molecular surface of AbirAc results in its poor solubility and plays an important role for retention of abiraterone in the cavity of the receptor formed by peptide chains and heme fragments. In order to evaluate the hydrolytic stability of AbirAc, to modify its solubility by formation of new solid forms and to model bonding of this medication with the heme, a series of d-metal complexes with AbirAc was obtained. AbirAc remains stable in water, acetonitrile, tetrahydrofuran, and ethanol, and readily interacts with dications as a terminal ligand to create discrete complexes, including [FePC(AbirAc)2] and [ZnTPP(AbirAc)] (H2PC = phthalocyanine and H2TPP = 5,10,15,20-tetraphenylporphyrine) models for ligand-receptor bonding. In reactions with silver(I) nitrate, AbirAc acts as a bridge ligand. Energies of chemical bonding between AbirAc and these cations vary from 97 to 235 kJ mol-1 and exceed those between metal atoms and water molecules. This can be indicative of the ability of abiraterone to replace solvent molecules in the coordination sphere of biometals in living cells, although the model [ZnTPP] complex remains stable in CDCl3, CD2Cl2, and 1,1,2,2-tetrachloroethane-d2 solvents and decomposes in polar dimethylsulfoxide-d6 and methanol-d4 solvents, as follows from the 1H DOSY spectra. Dynamics of its behavior in 1,1,2,2-tetrachloroethane-d2 were studied by ROESY and NMR spectra.
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Affiliation(s)
- Petr Buikin
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
- N. S. Kurnakov Institute of General and Inorganic Chemistry, RAS, 119991 Moscow, Russia
| | - Anna Vologzhanina
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
| | - Roman Novikov
- N. D. Zelinsky Institute of Organic Chemistry, RAS, 119991 Moscow, Russia;
| | | | - Alexander Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds, RAS, 119334 Moscow, Russia;
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8
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Chatterjee T, Mohammad M, Islam S, Mohammad Wabaidur S, Christy M, Maidul Islam M, Hedayetullah Mir M, Mafiz Alam S. Fabrication of a pyridyl appended linear Co(II) based coordination polymer: Structural insights and molecular docking. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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Vasile S, Roos K. Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors. ACS OMEGA 2023; 8:21438-21449. [PMID: 37360476 PMCID: PMC10285960 DOI: 10.1021/acsomega.2c08156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 06/28/2023]
Abstract
Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn2+ ions in the binding site of the influenza RNA polymerase PAN endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.
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Wróbel TM, Jørgensen FS, Pandey AV, Grudzińska A, Sharma K, Yakubu J, Björkling F. Non-steroidal CYP17A1 Inhibitors: Discovery and Assessment. J Med Chem 2023; 66:6542-6566. [PMID: 37191389 DOI: 10.1021/acs.jmedchem.3c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
CYP17A1 is an enzyme that plays a major role in steroidogenesis and is critically involved in the biosynthesis of steroid hormones. Therefore, it remains an attractive target in several serious hormone-dependent cancer diseases, such as prostate cancer and breast cancer. The medicinal chemistry community has been committed to the discovery and development of CYP17A1 inhibitors for many years, particularly for the treatment of castration-resistant prostate cancer. The current Perspective reflects upon the discovery and evaluation of non-steroidal CYP17A1 inhibitors from a medicinal chemistry angle. Emphasis is placed on the structural aspects of the target, key learnings from the presented chemotypes, and design guidelines for future inhibitors.
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Affiliation(s)
- Tomasz M Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Amit V Pandey
- Pediatric Endocrinology, Department of Pediatrics, University Children's Hospital, Inselspital, Bern and Translational Hormone Research Program, Department of Biomedical Research, University of Bern, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Angelika Grudzińska
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
| | - Katyayani Sharma
- Pediatric Endocrinology, Department of Pediatrics, University Children's Hospital, Inselspital, Bern and Translational Hormone Research Program, Department of Biomedical Research, University of Bern, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Jibira Yakubu
- Pediatric Endocrinology, Department of Pediatrics, University Children's Hospital, Inselspital, Bern and Translational Hormone Research Program, Department of Biomedical Research, University of Bern, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Gobbi S, Martini S, Rozza R, Spinello A, Caciolla J, Rampa A, Belluti F, Zaffaroni N, Magistrato A, Bisi A. Switching from Aromatase Inhibitors to Dual Targeting Flavonoid-Based Compounds for Breast Cancer Treatment. Molecules 2023; 28:3047. [PMID: 37049810 PMCID: PMC10096035 DOI: 10.3390/molecules28073047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Despite the significant outcomes attained by scientific research, breast cancer (BC) still represents the second leading cause of death in women. Estrogen receptor-positive (ER+) BC accounts for the majority of diagnosed BCs, highlighting the disruption of estrogenic signalling as target for first-line treatment. This goal is presently pursued by inhibiting aromatase (AR) enzyme or by modulating Estrogen Receptor (ER) α. An appealing strategy for fighting BC and reducing side effects and resistance issues may lie in the design of multifunctional compounds able to simultaneously target AR and ER. In this paper, previously reported flavonoid-related potent AR inhibitors were suitably modified with the aim of also targeting ERα. As a result, homoisoflavone derivatives 3b and 4a emerged as well-balanced submicromolar dual acting compounds. An extensive computational study was then performed to gain insights into the interactions the best compounds established with the two targets. This study highlighted the feasibility of switching from single-target compounds to balanced dual-acting agents, confirming that a multi-target approach may represent a valid therapeutic option to counteract ER+ BC. The homoisoflavone core emerged as a valuable natural-inspired scaffold for the design of multifunctional compounds.
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Affiliation(s)
- Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Martini
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Alessandra Magistrato
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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12
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Tolbatov I, Marrone A. Auranofin Targeting the NDM-1 Beta-Lactamase: Computational Insights into the Electronic Configuration and Quasi-Tetrahedral Coordination of Gold Ions. Pharmaceutics 2023; 15:pharmaceutics15030985. [PMID: 36986846 PMCID: PMC10057648 DOI: 10.3390/pharmaceutics15030985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Recently, the well-characterized metallodrug auranofin has been demonstrated to restore the penicillin and cephalosporin sensitivity in resistant bacterial strains via the inhibition of the NDM-1 beta-lactamase, which is operated via the Zn/Au substitution in its bimetallic core. The resulting unusual tetrahedral coordination of the two ions was investigated via the density functional theory calculations. By assessing several charge and multiplicity schemes, coupled with on/off constraining the positions of the coordinating residues, it was demonstrated that the experimental X-ray structure of the gold-bound NDM-1 is consistent with either Au(I)-Au(I) or Au(II)-Au(II) bimetallic moieties. The presented results suggest that the most probable mechanism for the auranofin-based Zn/Au exchange in NDM-1 includes the early formation of the Au(I)-Au(I) system, superseded by oxidation yielding the Au(II)-Au(II) species bearing the highest resemblance to the X-ray structure.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Paisos Catalans 16, 43007 Tarragona, Spain
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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13
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Abstract
Aquaporins (AQP) working as membrane channels facilitated water transport, play vital roles in various physiological progress including cell migration, energy metabolism, inflammation, etc. They are quite important drug targets, but elusive for discovery due to their undruggable properties. In this chapter, we summarized most fluently used methods for screening AQP inhibitors, including cell swelling assay, cell shrinking assay, and stopped-flow assay. And three classes of AQP inhibitors have been discussed, including metal-related inhibitors, quaternary ammonium salts, and small molecule inhibitors which further divided into four parts, sulfanilamide analogies, TGN-020, antiepileptic drugs, and others. It has been suggested that although they showed inhibition effects on AQP1, AQP3, AQP4, AQP7, or AQP9 in some researches, none of them could be asserted as AQP inhibitors to some extent. Discovering AQP inhibitors is a big challenge, but if successful, it will be a great contribution for human health.
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Affiliation(s)
- Shuyuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China
| | | | - Baoxue Yang
- School of Basic Medical Sciences, Peking University, Beijing, China.
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14
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Noor A, Qayyum S, Ali Z, Muhammad N. Syntheses and Structural Characterization of Divalent Metal Complexes (Co, Ni, Pd and Zn) of Sterically Hindered Thiourea Ligand and A Theoretical Insight of their Interaction with SARS-CoV-2 Enzyme. J Mol Struct 2022; 1274:134442. [PMID: 36337589 PMCID: PMC9621400 DOI: 10.1016/j.molstruc.2022.134442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
Abstract
Reacting two equivalents of sterically hindered 1,3-bis(2,6-diethylphenyl)thiourea ligand (L) with CoCl2, NiBr2, PdX2 (X = Cl; Br) and ZnI2 in acetonitrile afforded the corresponding bulky thiourea ligand stabilized four coordinated monomeric [L2CoCl2] (1), [L2NiBr2] (2), [L2PdX2] (3a: X = Cl; 3b: X = Br) and [L2ZnI2] (4.2CH3CN) complexes. Compound 1, 2 and 4.2CH3CN are tetrahedral whereas Pd complexes (3a and 3b) are square planar. In solution, palladium complexes are dominated by cis-isomers. Structural characterization shows inter- and intramolecular hydrogen bonding. Hirshfeld surface and fingerprint plots indicated significant intermolecular interactions in the crystal network. Molecular docking analysis revealed relatively higher SARS-CoV-2 enzyme interacting abilities of the synthesized complexes compared to the free ligand. All compounds have been characterized by elemental analyses, NMR spectroscopy and single-crystal X-ray diffraction.
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Affiliation(s)
- Awal Noor
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia,Corresponding Author:
| | - Sadaf Qayyum
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, 31982 Al-Hassa, Saudi Arabia
| | - Zafar Ali
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Niaz Muhammad
- Department of Chemistry, Abdul Wali Khan University, Mardan, KPK, Pakistan
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15
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Caciolla J, Martini S, Spinello A, Belluti F, Bisi A, Zaffaroni N, Magistrato A, Gobbi S. Single-digit nanomolar inhibitors lock the aromatase active site via a dualsteric targeting strategy. Eur J Med Chem 2022; 244:114802. [DOI: 10.1016/j.ejmech.2022.114802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022]
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16
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Lengacher R, Marlin A, Śmiłowicz D, Boros E. Medicinal inorganic chemistry - challenges, opportunities and guidelines to develop the next generation of radioactive, photoactivated and active site inhibiting metal-based medicines. Chem Soc Rev 2022; 51:7715-7731. [PMID: 35942718 DOI: 10.1039/d2cs00407k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Medicinal inorganic chemistry is a burgeoning subfield of medicinal chemistry that focuses on the development of metal-based diagnostic and therapeutic agents. This tutorial review aims to provide an introductory primer, present a timely overview of recent discoveries and identify current challenges and opportunities of the field. Three specific areas of discovery are highlighted herein. The first part focuses on metal-based radiopharmaceuticals for diagnostic and therapeutic purposes and specific design criteria for the development of radiopharmaceuticals that combine fundamental aqueous coordination chemistry with elucidation of pharmacokinetics. The second part describes approaches to photodynamic therapy with metal complexes. Here, photophysical characterization, combined with the challenge of careful control of the chemical behavior and selective biological deposition of transition metals with significant off-target toxicity, is discussed. In the third part, we summarize emerging strategies to modulate enzyme inhibition with coordination chemistry, while also highlighting the utility of the unique properties of metal ions for the characterization of mechanisms of action of these emerging diagnostic and therapeutic agents.
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Affiliation(s)
- Raphael Lengacher
- Department of Chemistry, Stony Brook University, Stony Brook, 11790 New York, USA.
| | - Axia Marlin
- Department of Chemistry, Stony Brook University, Stony Brook, 11790 New York, USA.
| | - Dariusz Śmiłowicz
- Department of Chemistry, Stony Brook University, Stony Brook, 11790 New York, USA.
| | - Eszter Boros
- Department of Chemistry, Stony Brook University, Stony Brook, 11790 New York, USA.
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17
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Jiang M, Zhang Z, Li W, Man X, Sun H, Liang H, Yang F. Developing a Copper(II) Agent Based on His-146 and His-242 Residues of Human Serum Albumin Nanoparticles: Integration To Overcome Cisplatin Resistance and Inhibit the Metastasis of Nonsmall Cell Lung Cancer. J Med Chem 2022; 65:9447-9458. [PMID: 35786921 DOI: 10.1021/acs.jmedchem.2c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To overcome the resistance of nonsmall cell lung cancer (NSCLC) cells to cisplatin and inhibit their metastasis, we proposed to develop a Cu(II) agent based on the specific residue(s) of HSA nanoparticles (NPs) for multitargeting the tumor microenvironment (TME). To this end, we not only synthesized four Cu(II) 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone compounds (C1-C4), obtaining a Cu compound (C4) with significant cytotoxicity by studying their structure-activity relationships, but also revealed the binding mechanism of C4 to HSA through X-ray crystallography and confirmed the successful construction of a new HSA-C4 NPs delivery system. C4 and HSA-C4 NPs inhibited the A549cisR tumor growth and metastasis, and HSA NPs optimized the anticancer behavior of C4. We further confirmed the anticancer mechanism of the C4/HSA-C4 NP multitargeting TME to overcome cisplatin resistance: killing tumor cells by acting on the mtDNA and inducing apoptosis, polarizing M2-type macrophages to the M1-type, and inhibiting angiogenesis.
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Affiliation(s)
- Ming Jiang
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China.,School of Food and Biochemical Engineering, Guangxi Science & Technology Normal University, Laibin, Guangxi 546199, China
| | - Zhenlei Zhang
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Wenjuan Li
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Xueyu Man
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Hong Liang
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Feng Yang
- School of Chemistry and Pharmaceutical Sciences, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, Guangxi Normal University, Guilin, Guangxi 541004, China
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18
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Fan Y, Kao C, Yang F, Wang F, Yin G, Wang Y, He Y, Ji J, Liu L. Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer. Front Oncol 2022; 12:899900. [PMID: 35761863 PMCID: PMC9232398 DOI: 10.3389/fonc.2022.899900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background With the rapid development and wide application of high-throughput sequencing technology, biomedical research has entered the era of large-scale omics data. We aim to identify genes associated with breast cancer prognosis by integrating multi-omics data. Method Gene-gene interactions were taken into account, and we applied two differential network methods JDINAC and LGCDG to identify differential genes. The patients were divided into case and control groups according to their survival time. The TCGA and METABRIC database were used as the training and validation set respectively. Result In the TCGA dataset, C11orf1, OLA1, RPL31, SPDL1 and IL33 were identified to be associated with prognosis of breast cancer. In the METABRIC database, ZNF273, ZBTB37, TRIM52, TSGA10, ZNF727, TRAF2, TSPAN17, USP28 and ZNF519 were identified as hub genes. In addition, RPL31, TMEM163 and ZNF273 were screened out in both datasets. GO enrichment analysis shows that most of these hub genes were involved in zinc ion binding. Conclusion In this study, a total of 15 hub genes associated with long-term survival of breast cancer were identified, which can promote understanding of the molecular mechanism of breast cancer and provide new insight into clinical research and treatment.
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Affiliation(s)
- Yeye Fan
- School of Mathematics, Shandong University, Jinan, China
| | - Chunyu Kao
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fu Yang
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fei Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Gengshen Yin
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yongjiu Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yong He
- School of Mathematics, Shandong University, Jinan, China.,Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Jiadong Ji
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Liyuan Liu
- School of Mathematics, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
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19
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Khatua S, Taraphder S. In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II. J Biomol Struct Dyn 2022; 41:3187-3204. [PMID: 35257634 DOI: 10.1080/07391102.2022.2048075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The crystal structure of human carbonic anhydrase (HCA) II bound to an inhibitor molecule, 6-hydroxy-2-thioxocoumarin (FC5), shows FC5 to be located in a hydrophobic pocket at the active site. The present work employs classical molecular dynamics (MD) simulation to follow the FC5 molecule for 1 μs as it unbinds from its binding location, adopts the path of substrate/product diffusion (path 1) to leave the active site at around 75 ns. It is then found to undergo repeated binding and unbinding at different locations on the surface of the enzyme in water. Several transient excursions through different regions of the enzyme are also observed prior to its exit from the active site. These transient paths are combined with functionally relevant cavities/channels to enlist five additional pathways (path 2-6). Pathways 1-6 are subsequently explored using steered MD and umbrella sampling simulations. A free energy barrier of 0.969 kcal mol-1 is encountered along path 1, while barriers in the range of 0.57-2.84 kcal mol-1 are obtained along paths 2, 4 and 5. We also analyze in detail the interaction between FC5 and the enzyme along each path as the former leaves the active site of HCA II. Our results indicate path 1 to be the major exit pathway for FC5, although competing contributions may also come from the paths 2, 4 and 5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Satyajit Khatua
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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20
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López R, Díaz N, Francisco E, Martín-Pendás A, Suárez D. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. J Chem Inf Model 2022; 62:1510-1524. [PMID: 35212531 PMCID: PMC8965874 DOI: 10.1021/acs.jcim.1c01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
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Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Facultad de Biología, Campus de Vegazana s/n, 24071 León (Castilla y León), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Angel Martín-Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
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21
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Tolbatov I, Marrone A, Coletti C, Re N. Computational Studies of Au(I) and Au(III) Anticancer MetalLodrugs: A Survey. Molecules 2021; 26:7600. [PMID: 34946684 PMCID: PMC8707411 DOI: 10.3390/molecules26247600] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/29/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022] Open
Abstract
Owing to the growing hardware capabilities and the enhancing efficacy of computational methodologies, computational chemistry approaches have constantly become more important in the development of novel anticancer metallodrugs. Besides traditional Pt-based drugs, inorganic and organometallic complexes of other transition metals are showing increasing potential in the treatment of cancer. Among them, Au(I)- and Au(III)-based compounds are promising candidates due to the strong affinity of Au(I) cations to cysteine and selenocysteine side chains of the protein residues and to Au(III) complexes being more labile and prone to the reduction to either Au(I) or Au(0) in the physiological milieu. A correct prediction of metal complexes' properties and of their bonding interactions with potential ligands requires QM computations, usually at the ab initio or DFT level. However, MM, MD, and docking approaches can also give useful information on their binding site on large biomolecular targets, such as proteins or DNA, provided a careful parametrization of the metal force field is employed. In this review, we provide an overview of the recent computational studies of Au(I) and Au(III) antitumor compounds and of their interactions with biomolecular targets, such as sulfur- and selenium-containing enzymes, like glutathione reductases, glutathione peroxidase, glutathione-S-transferase, cysteine protease, thioredoxin reductase and poly (ADP-ribose) polymerase 1.
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Affiliation(s)
- Iogann Tolbatov
- Institut de Chimie Moleculaire de l’Université de Bourgogne (ICMUB), Université de Bourgogne Franche-Comté (UBFC), Avenue Alain Savary 9, 21078 Dijon, France;
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi “G. D’Annunzio” Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy; (A.M.); (C.C.)
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università degli Studi “G. D’Annunzio” Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy; (A.M.); (C.C.)
| | - Nazzareno Re
- Dipartimento di Farmacia, Università degli Studi “G. D’Annunzio” Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy; (A.M.); (C.C.)
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22
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Medina FE, Jaña GA. QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fabiola E. Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
- Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, 4051381 Concepción, Chile
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
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23
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Hruby M, Martínez IIS, Stephan H, Pouckova P, Benes J, Stepanek P. Chelators for Treatment of Iron and Copper Overload: Shift from Low-Molecular-Weight Compounds to Polymers. Polymers (Basel) 2021; 13:3969. [PMID: 34833268 PMCID: PMC8618197 DOI: 10.3390/polym13223969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/18/2022] Open
Abstract
Iron and copper are essential micronutrients needed for the proper function of every cell. However, in excessive amounts, these elements are toxic, as they may cause oxidative stress, resulting in damage to the liver and other organs. This may happen due to poisoning, as a side effect of thalassemia infusion therapy or due to hereditary diseases hemochromatosis or Wilson's disease. The current golden standard of therapy of iron and copper overload is the use of low-molecular-weight chelators of these elements. However, these agents suffer from severe side effects, are often expensive and possess unfavorable pharmacokinetics, thus limiting the usability of such therapy. The emerging concepts are polymer-supported iron- and copper-chelating therapeutics, either for parenteral or oral use, which shows vivid potential to keep the therapeutic efficacy of low-molecular-weight agents, while avoiding their drawbacks, especially their side effects. Critical evaluation of this new perspective polymer approach is the purpose of this review article.
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Affiliation(s)
- Martin Hruby
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic Heyrovského Náměstí 2, 162 06 Prague, Czech Republic;
| | - Irma Ivette Santana Martínez
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research Bautzner Landstraße 400, 01328 Dresden, Germany; (I.I.S.M.); (H.S.)
| | - Holger Stephan
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research Bautzner Landstraße 400, 01328 Dresden, Germany; (I.I.S.M.); (H.S.)
| | - Pavla Pouckova
- Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University in Prague, Salmovska 1, 120 00 Prague, Czech Republic; (P.P.); (J.B.)
| | - Jiri Benes
- Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University in Prague, Salmovska 1, 120 00 Prague, Czech Republic; (P.P.); (J.B.)
| | - Petr Stepanek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic Heyrovského Náměstí 2, 162 06 Prague, Czech Republic;
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24
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Pinto A, Roma-Rodrigues C, Ward JS, Puttreddy R, Rissanen K, Baptista PV, Fernandes AR, Lima JC, Rodríguez L. Aggregation versus Biological Activity in Gold(I) Complexes. An Unexplored Concept. Inorg Chem 2021; 60:18753-18763. [PMID: 34719915 DOI: 10.1021/acs.inorgchem.1c02359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aggregation process of a series of mono- and dinuclear gold(I) complexes containing a 4-ethynylaniline ligand and a phosphane at the second coordination position (PR3-Au-C≡CC6H4-NH2, complexes 1-5, and (diphos)(Au-C≡CC6H4-NH2)2, complexes 6-8), whose biological activity was previously studied by us, has been carefully analyzed through absorption, emission, and NMR spectroscopy, together with dynamic light scattering and small-angle X-ray scattering. These experiments allow us to retrieve information about how the compounds enter the cells. It was observed that all compounds present aggregation in fresh solutions, before biological treatment, and thus they must be entering the cells as aggregates. Inductively coupled plasma atomic emission spectrometry measurements showed that mononuclear complexes are mainly found in the cytosolic fraction; the dinuclear complexes are mainly found in a subsequent fraction composed of nuclei and cytoskeleton. Additionally, dinuclear complex 8 affects the actin aggregation to a larger extent, suggesting a cooperative effect of dinuclear compounds.
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Affiliation(s)
- Andrea Pinto
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain.,Institut de Nanociència i Nanotecnologia (IN2UB). Universitat de Barcelona, 08028 Barcelona, Spain
| | - Catarina Roma-Rodrigues
- UCIBIO─Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Jas S Ward
- Department of Chemistry, University of Jyvaskyla, P.O. Box 35, 40014 Jväskylä, Finland
| | - Rakesh Puttreddy
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101 Tampere, Finland
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, P.O. Box 35, 40014 Jväskylä, Finland
| | - Pedro V Baptista
- UCIBIO─Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO─Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.,Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - João Carlos Lima
- LAQV-REQUIMTE, Departamento de Química, CQFB, Universidade Nova de Lisboa, 2825-152 Monte de Caparica, Portugal
| | - Laura Rodríguez
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain.,Institut de Nanociència i Nanotecnologia (IN2UB). Universitat de Barcelona, 08028 Barcelona, Spain
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Pirc K, Hodnik V, Snoj T, Lenarčič T, Caserman S, Podobnik M, Böhm H, Albert I, Kotar A, Plavec J, Borišek J, Damuzzo M, Magistrato A, Brus B, Sosič I, Gobec S, Nürnberger T, Anderluh G. Nep1-like proteins as a target for plant pathogen control. PLoS Pathog 2021; 17:e1009477. [PMID: 33857257 PMCID: PMC8078777 DOI: 10.1371/journal.ppat.1009477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/27/2021] [Accepted: 03/14/2021] [Indexed: 11/19/2022] Open
Abstract
The lack of efficient methods to control the major diseases of crops most important to agriculture leads to huge economic losses and seriously threatens global food security. Many of the most important microbial plant pathogens, including bacteria, fungi, and oomycetes, secrete necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs), which critically contribute to the virulence and spread of the disease. NLPs are cytotoxic to eudicot plants, as they disturb the plant plasma membrane by binding to specific plant membrane sphingolipid receptors. Their pivotal role in plant infection and broad taxonomic distribution makes NLPs a promising target for the development of novel phytopharmaceutical compounds. To identify compounds that bind to NLPs from the oomycetes Pythium aphanidermatum and Phytophthora parasitica, a library of 587 small molecules, most of which are commercially unavailable, was screened by surface plasmon resonance. Importantly, compounds that exhibited the highest affinity to NLPs were also found to inhibit NLP-mediated necrosis in tobacco leaves and Phytophthora infestans growth on potato leaves. Saturation transfer difference-nuclear magnetic resonance and molecular modelling of the most promising compound, anthranilic acid derivative, confirmed stable binding to the NLP protein, which resulted in decreased necrotic activity and reduced ion leakage from tobacco leaves. We, therefore, confirmed that NLPs are an appealing target for the development of novel phytopharmaceutical agents and strategies, which aim to directly interfere with the function of these major microbial virulence factors. The compounds identified in this study represent lead structures for further optimization and antimicrobial product development.
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Affiliation(s)
- Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tina Snoj
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tea Lenarčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Simon Caserman
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Hannah Böhm
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Isabell Albert
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia
| | - Jure Borišek
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Martina Damuzzo
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Boris Brus
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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